The site is sacred to both Muslims and Jews and as such is a recurrent flashpoint in the Arab-Israeli conflict.
Israeli Prime Minister Benjamin Netanyahu's cabinet voted Monday night to dismantle metal detectors set up outside al-Aqsa in response to an attack there by an Arab gunman that killed two Israeli police officers on 14 July.
Palestinians alleged Israel was trying to expand its control at the Muslim administered site, which is overseen by neighbouring Jordan. Israel has denied the accusations.
Attempts to deny Muslim men under the age of 50 access to the site for prayers led to mass protests in the contested capital.
Four Palestinians were killed in street clashes and three Israeli settlers were killed in their West Bank home in the ensuing unrest. On Sunday, two Jordanians were killed after one attacked a guard at the Israeli embassy in Amman with a screwdriver.
"From here I make a call to all Muslims. Anyone who has the opportunity should visit Jerusalem, Al-Aqsa mosque,” Mr Erdogan said in Ankara. “Come, let’s all protect Jerusalem", he added.
Mr Erdogan also criticised what he said was the use of "excessive" Israeli force to break up recent street protests.
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